Happy Holidays!

So yeah, I’m about as non-religious as you can get, but that doesn’t mean I don’t appreciate the holiday spirit! Today is a great day for appreciating the “blessings” of the past year and the family with which we surround ourselves.

Traditionally, this is the day that I start to think about new years resolutions, if I can think of any that appeal to me. Usually, I can pull off the ones that I commit to, ,which makes it a useful exercise. My most successful resolution was about 5 years ago, when I made the solitary resolution to be more outspoken. I’d say that I’ve done pretty well at it. (-:

Hopefully, this year I can come up with a few more that work, such as blogging more, reading more papers, writing more papers, finishing my thesis, getting a job… well, ok, those aren’t all really resolutions, but hey, it’s all on tap for 2011. Should be a good year.

In the meantime, have a great holiday, everyone, and I look forward to hearing your resolutions for the New Years!

Debunking a new twtitter follwer, IslamNederland

I’ve been a little more outspoken about my belief (or lack thereof) as an atheist lately. I don’t know if that will come back to bite me when it comes time to find a job in the future, but it’s a part of who I am – and I don’t want to censor myself too much. I suppose my recent talk about religion may be why I picked up a new follower today on twitter: IslamNederland. I can’t imagine that this individual will follow me for long, since we have such divergent viewpoints, but it provided me with a bit of a distraction this afternoon.

When I receive an email from twitter letting me know that someone is following me, I usually take a look over at their twitter page. If there’s anything new and interesting on it that I’ve not seen through anyone else that I follow, I’ll most likely subscribe. It’s a pretty quick filter for me – about 1/3rd of the people who follow me don’t have public tweets, and I’m pretty shy about asking people to open their twitters up to me when all I know about them is what they have on their bio.

Anyhow, seeing IslamNederland’s tweets threw me for a loop. Not only are they proposing a religion that I feel is as silly as any other, the tweets include a few blatant.. um.. creative use of facts. Thus, I thought I’d spend a few minutes to debunk a few of them. Try this one on for size:

IslamNederland says: You’re telling me that an eclipse where the moon exactly blocks the sun in size had no intention to do that and is just a mere coincidence?

Actually, YES! But, more than that, I have to question the very premise of this tweet on several levels:
1. Finding a single (non-repeating) pattern in the chaos of the universe is not a good proof of god. If it were so, a complete lack of pattern would prove all gods’ non-existence… and there are an infinite number of “irrational” numbers, such as Pi (the ratio of a circle’s circumference to it’s radius) and e, and Phi. Each of those lacks a pattern – so they’re clearly not ‘s work. Tada – God didn’t create all numbers!
2. Are you aware that not all eclipses are “exactly” blocking the sun? The earth’s orbit is not a perfect circle: it’s an eclipse. Thus, there’s such a thing as an annular eclipse, where the moon fails to block out the sun completely, leaving a ring of the sun showing.
3. Over time, this will change. Sure, it might take several millions of years, but the orbits of the earth and the moon are slowly changing, and eventually those ratios will not even look as close as they do today. Does that mean god will have abandoned us?


IslamNederland says: When men stop believing in God they don’t believe in nothing; they believe in anything – G. K. Chesterton.

Frankly, this would be an appeal to authority. Someone said it, therefore it must be true. However, most atheists are atheists because they refuse to believe in a god without real evidence beyond scripture and appeal to patterns. (Is there a better name for the “it can’t be coincidence fallacy”?) Thus, suggesting that a lack of belief in the irrational means that you’ll believe anything irrational is just illogical – and rather insulting to boot.

Moving right along…

IslamNederland says: For atheism our existence is without any purpose or at best it is to propagate DNA. So what is the difference between us & a swarm of flies?

Well, from a biology point of view, there are an awful lot of things that separate us from a swarm of flies – just at the macroscopic level alone we share very little in common physically. Personally, I have no problem swatting a fly because I know how much they lack in terms of intelligence. They exist to eat, procreate and spoil my food, and I’m not happy to have them in my kitchen.
On the other hand, there is much we share in common at the DNA level. We use many of the same genes to do many of the same functions – DNA repair, transcription factors, histones, etc. All life on earth shares a common ancestor, so if your point is to say that we’re special just because we’re human, then you’re way off the mark.
At the risk of ranting, if we were designed specially, why didn’t we get better eyes, like those of an octopus? Why aren’t we born without the vestigial appendix? Why does our vegas nerve take the path it does? Clearly, the human anatomy doesn’t lend itself to design over evolution.
Fundamentally, biology doesn’t tell us we’re the same at flies – we have our strengths, as do flies, but it also doesn’t tell us we’re anything other than human, with human senses, feelings and emotions. I can live with that.

How about this one?

IslamNederland says: The cure for ignorance is asking

Actually, no. The cure for ignorance is research. Asking someone else doesn’t tell you the real answer – it tells you someone’s opinion. Of course, you can ask someone else who has done the research and can show the results of their research, which is the foundation of peer review and science. Otherwise, as we all know, accepting someone else’s opinion blindly is the best way to pass on superstitions and religions, but not the best way to find out how things really work.

How about this next one as a font of wisdom?

IslamNederland says: If everybody sticks to the Islamic marriage system, AIDS will be history within a few generations. The only real solution

I find this disturbing. Right up there with other bad ideas such as all of us becoming Catholics so that we wouldn’t have to worry about sectarian violence. The most disturbing part of this is the underlying assumption that we should all adopt Islam’s (or any one culture’s) version of morals to solve a medical problem. Frankly, I find sharia law to be barbaric (cutting off hands for theft, stoning people, and blaming the victim of rape… I’m filing this under “ethics fail”.), so I’m just going to have to toss this idea into the reject bin. More on that in the next reply, so lets move right along.

IslamNederland says: Zion Zohar: “when Muslims crossed Gibraltar in 711 n invaded Iberian Peninsula, Jews welcomed them as liberators from Christian Persecution”

Actually, while this may be correct, it’s not even close to being relevant in today’s society, which I suspect is the implication here. Frankly, in 711, Europe was in the midst of the dark ages, when religion was at its most oppressive and the Muslims had had less than 100 years since their prophet’s death to begin calcifying into the repressive religion it appears to have become today. (Yes, I’m painting with a broad bush – there are many exceptions.) I’m aware of the prophet himself having given charters to Christian monasteries in the name of tolerance – something that some sects of Islam have failed to keep up. Let me ask, would the Jews welcome the Iranians as liberators if they were to march on Jerusalem today? I’m thinking no. Frankly, while Sharia law may have been less barbaric than what the medieval Christians were practising at the time, secular laws are VASTLY better than anything available in the 7th century.

I’m all for people teaching tolerance and respect for ALL of their fellow human beings (and the animals too), but lets do it without the make believe and superstition – and foremost: without the lies/errors.

Ok, I think that will do for tonight. Lest anyone think I take issue only with the Muslim faith, I’d be more than happy to try to correct factual errors that I can for any faith. Cheers!

A salute to IDEs.

Not that this will mean much to anyone but coders, but it was a startling revelation to me. After mainly doing code development in Java using the eclipse IDE (Integrated development environment, for the non-coders) for a couple of years, I’ve become pretty “soft” as a programmer.. When your IDE prompts you for function names, does imports and stuff, you can code pretty quickly, and the quality of your code is going to be relatively high. After all, you can focus on the algorithms and not worry about leaving silly typos in your code. (Bugs yes, typos not so much.)

However, since this weekend, I’ve been hacking around with data visualization using javascript/HTML5 – which, as far as I know, doesn’t have a Linux IDE for development. Hence, I’m writing code in the nano editor. (If you used email in the early nineties, nano looks just like the pine email client.) Unlike my “cushy” java IDE where function names come up automatically, working in nano means I need to memorize the name of every function I want to use.

Even worse, nano doesn’t display the code with proper formatting – it just assumes the whole thing is html and thus messes around with colours (making everything a dark, unreadable blue) every time I use a less-than (“<") symbol. Anyhow, even with the total lack of a decent IDE, I've still managed to write a couple hundred lines of code and have some neat but pre-mature animations. But... Unfortunately, I'm spending equal amounts of time looking up functions, testing code, and trying to debug typos. Coding this way is just like developing in pascal in 1992, except back then I had only a help file with no search function, whereas google is now my best friend. At any rate, I would like to take this opportunity to say thank you to the people who write IDEs. Like human rights and basic freedoms, you never appreciate your tools fully until you have to live without them.

And the clueless award goes to… the pope!

Alright, so the media often get things wrong, but I’d like to share this article where the pope claims secularism as a threat to humanity as great as fanatical religions – which is about as stupid as you can get. It’s possible that the pope has been misquoted, but in light of his other hate filled speeches, which have blamed the worlds ills on secularists, I somehow doubt it.

Unlike what the pope would have you think, I don’t see secular proponents bombing airplanes, trying to pass laws to discriminate against religions or spread disease… although the pope seems to think it’s happening.

I really don’t get his point. Where are the oppressed Christians, struggling with oppressors who are trying to marginalize them? All I see is the secularists trying to tell the Christians to stop beating on the jews, homosexuals, poor and needy – and somehow that’s a bad thing?

I’m sorry, Mr. Pope, but I’m not really interested in returning to the dark ages where inquisitions were allowed. However, I suppose I should be happy that you’ve finally noticed that the western world has left you behind. The bright and shiny bonus, however, should be that it seems Europe is doing well to discover that the church doesn’t have the answers it pretends to.

the circle of life..

When I was getting close to the end of my masters degree, a fellow graduate student pulled me aside and asked me if I could think of any algorithms for a quantum computer… That turned into a rather successful biotechnology company here in Vancouver. As far as I was concerned, the quantum computer never materialised – but I don’t think they were necessary for that company. It would have been a nice touch, but it was never a core part of the strategy.

Now, as I near the end of my PhD, my supervisor asked me the same question today. Unfortunately, I’m still not sure that there’s a good answer to it either. I can think of great things I’d like to do with a quantum computer, but I still face the same problems as the first time around:

A) Does it actually exist?
B) When will it be ready?
and C) what can it do?

Coming up with problems is easy – coming up with problems that take advantage of an imaginary computer with imaginary strengths (of which I know very little) is hard.

Somehow, I don’t see this leading to a chapter in my theis. At least, this time, I don’t think I’ll lead to a start up company.

Why Nobel Prize winners can go rogue and why I could be a quackpot.

Following various tweets and links over the weekend took me through several interesting articles on Nobel Prize winners who go over the deep end. In particular, I’d like to talk about this one:

Luc Montagnier: The Nobel disease strikes again – a post on the Respectful Insolence blog.

I thought the article was well written and I thoroughly enjoyed seeing some quackery reduced to it’s baseline incoherent principles. It’s a great combination of fantastic writing and excellent discussion of both science and ethics of Dr. Montagnier’s quackpottery.

However, I would like to expand on the author’s final conclusion:

I’ve wondered how some Nobel Laureates, after having achieved so much at science, proving themselves at the highest levels by making fundamental contributions to our understanding of science that rate the highest honors, somehow end up embracing dubious science (Ignarro) or even outright pseudoscience (Pauling or Montagnier). Does the fame go to their head? Do they come to think themselves so much more creative than other scientists that their fantastical ideas become plausible to them? Does winning the Nobel Prize lead some scientists to think that the genius they showed in their own area of expertise that allowed them to win such an exalted prize also applies to other areas of science outside their area of expertise? Who knows?

Frankly, I think the author has hit upon the answer in his last point. Science is not a field that necessarily encourages creativity and outside of the box thinking. Many scientists are good at seeing what the data presents to them and not a lot more. The Nobel Prize stands out as a way to recognise unusual insight, fantastic creativity and attention to the unexpected – it is the scientific way to encourage those thinkers who can take on established science thought patterns and challenge our expectations of what is going on.

No surprise, then, that many of the people who are willing to think outside of the box and ignore scientific conventions find themselves willing to do it again. As the author of the blog post points out, they were rewarded for it once, so why not do it again?

That is to say, the very same characteristics that made them Nobel Prize candidates are the ones that make them potential quackpots!

Thus, the bigger question for me is why more of them don’t go over the deep end – and I think that’s the more enlightening answer. Normally, we hammer into scientists the need for critical thinking in evaluating the papers, abstracts and communications that make up the body of scientific literature – however, I suspect that many of the scientists I’ve known have failed to utilise the same skills on their own thought processes.

That is to say, one shouldn’t form an opinion without some form of evidence to back up their claims – or more concisely put, one should not only be a sceptic when hearing claims, but also when forming them too!

And that, I think is the grand test for future quackpottery. If you’re willing to form opinions and state them before the evidence is in, you’re either a Nobel Prize candidate or a future quackpot – or both! (Please note the clarification that most if not all Nobel Prize winners DO confirm their findings before publishing, and I am not slighting their work in the least!)

Of course, if you’re reading this, you’ll probably recognise the ultimate irony of it – I’m not a psychologist, a Nobel Prize winner, or a doctor of any type, yet I’m weighing in on the subject without access to any Nobel Prize winners to test out my theories. Indeed, that means I’ve failed my own test for quackpottery.

If Sequencing technologies were food…

Over the years, I’ve become more of a foodie than I used to be. I always had an interest in food, but it wasn’t until I started cooking for my wife after we met back in 2002 that I started investing the time and energy into it.

In any case, I got to thinking about what kind of food best describes each Next-gen sequencing technology. Yes, it’s silly, but hey – it’s fun! Here goes.

In no particular order:

  • Complete Genomics – Meatloaf: Complete Genomics is a love hate relationship for me. They’re the company that most understands social media, that has the most realistic vision of their technology, and a simple plan for moving forward. Like meatloaf, they may well be the food for the masses. However, they’re also the one company that has the least exciting technology. Yes, they are doing neat things with their tech – but the technology isn’t going to surprise anyone who studied biochemistry in the 1990’s. They really are the boring meatloaf of the sequencing world – but wow, who knew you could do that with meatloaf?
  • Illumina – sushi: If you don’t live on the west coast, you might not get this. Here, in Vancouver, sushi is a staple. There’s a sushi restaurant on every corner, competing with Starbucks for real estate. When I think of Illumina, sushi just makes sense as a good comparison: the machines are plentiful, and the quality can vary according to where you go. The early illumina sequencing data sets kinda left an off-taste in your mouth, but the quality has increased while the price has dropped, just like sushi. Also like sushi, Illumina is clearly the mainstay, and about as plentiful as the sushi shops in Vancouver. mmm…sushi.
  • 454/pyrosequencing – Greasy diner food: You know, diner food is hit or miss. My first next-gen experiences were with 454, and in hindsight, were a complete waste of time. That’s not to say it’s all garbage, but like Illumina, it had to mature. If you’ve ever watched the food network, you’ll probably have come across the show “Diners, Drive-ins and Dives”, you’ll know that you can get some pretty high-end greasy diner food. For me, 454 has gone from the worst of the dives to being a pretty decent greasy-spoon. I wouldn’t want to eat it every meal, but I’m happy to do it once in a while, as long as we balance it with some veggies, or maybe some sushi. (-:
  • SOLiD – Chinese food: Most people think of stuff like Lemon-Chicken, or spring rolls as typical chinese food, but SOLiD reminds me of Chinese wedding food. It’s finicky and doesn’t always work – and isn’t accessible for everyone. eg. Chicken Feet just isn’t my thing. Of course, if you’re a chinese banquet chef, you can get it working and you get some pretty fantastic food, but it seems that it takes a lof of finicky work to get it looking and tasting good. Those who like it like it, like it a lot. Much like Chinese food, you either get it or you don’t. My limited experience with SOLiD data tells me that it’s a pain in the back end to work with, but pretty rewarding when it finally all comes together.
  • Pacific Biosciences – SoufflĂ©.: I still think of PacBio as my favourite of the technologies. It’s the one that I most want to see succeed, and that has the most “neat” technology. Kind of having Star Trek technology materialise in front of your eyes. Unfortunately, it’s also the one that appears to have the most roadblocks in the sense that it seems hardest to get good meaning out of. As a food, for me, it would be a soufflĂ©. Personally, I’m not sure how much effort would be required to get it to work, nor if the end result will be the perfect meal or if it’ll all collapse flat and fail miserably. That said, I know it has the potential to be the best damn meal ever, if only the risk/uncertainty can be surmounted.
  • Oxford Nanopore – Astronaut ice-cream: Nanopore is the food that everyone tells me is great, that is completely space-age, completely revolutionary – and yet I just don’t see it at the grocery store. The concept is neat, but I just don’t know who’s buying it yet. Is it even available? Obviously I’m shopping at the wrong place.
  • Ion Torrent – A baguette… after MacGyver has jury rigged it to be the wings of a supersonic air plane. That is to say, they’ve made something fantastic out of what appear to be very basic ingredients. Seriously, they do some neat stuff with computer chips and it is pretty damn cool. They’ve used what appears to be off the shelf parts and some seriously fantastic engineering to deliver a really awesome platform. What can I say, I’m looking forward to sandwiches sponsored by Ion Torrent at a conference one day – it’ll be some fine food, I’m sure.
  • Sanger/ABI – McDonalds basic burger: I probably didn’t need to include this one, but it’s pretty clear where it’s at. Using Sanger sequencing today is pretty un-fulfilling. It’s cheap, it’s quick, and it just takes care of a very minimal need. Much like the assembly line burger at McDonalds – it’ll fill you up and take care of a burning hunger… but it’s not gourmet, and leaves you less than filled – but it’s cheap. I’m not convinced it’s more reliable than any the next gen – but it’s familiar and consistent.

All in all, it’s a pretty strange menu. Did I miss anything? Feel free to add your own food analogies.

Occam’s Typewriter…

Just in case there’s anyone who reads my blog who’s been on a transatlantic flight, or trapped in a mine.. or by some other excuse hasn’t seen twitter or the net all day, I wanted to bring a new Blog Consortia to your attention.

Naturally, all new blog groups have to come up with ever-increasingly cooler names. This one is no exception: Occams’ typewriter is clearly the best name I’ve heard yet. (Indeed, I’m jealous that I haven’t figured out how to get Occam’s name into my own blog title yet.)

Furthermore, several of my favorite bloggers are now there: Richard Grant (aka “Confessions of a (former) Lab Rat”), Cath Ennis (is it Ok to use your last name here?) (aka “VWXYNot?” and Erika Cule of “Blogging the PhD”. In fact, I highly suggest checking out the other bloggers as well.

Unfortunately for the typewriter crew, I think that the move to their new home was a bit premature, and likely caused by yet another Nature Blogs bug – while I can still get over to my blog over there, it seems many others were accidentally locked out. Despite the premature move, I think they’re off to a great start. I’m looking forward to many excellent posts and discussions.

Good luck guys, be careful wielding your razors, typewriters and other implements of destruction.

Today’s Music of the Day – Carmina Burana

Another one of my favorite pieces in the classical style is Carmina Burana. It has a neat history, with the texts having been found in a monastery and later put to music by Carl Orf. One of the most popular parts of the music is the “O Fortuna” piece, frequently used in movies that want a medieval sounding theme.

One of my favourite musical passages of all time is at 40:12 in this video, the “In taberna quando sumus”. It’s an incredibly odd piece of music, but just works somehow.

Next Gen Course Material

I stumbled upon some really neat presentations that are in use for a week (?) long course in next gen sequencing called ANGUS. I took a look through a few presentations and was rather impressed. Though, I should say that a lot of the slides in the chip-seq section came straight from my blog – so hey, that’s pretty cool.

In any case, if you have a few minutes and need a quick introduction to any next gen topics, you should check it out.

Here are all of the presentations, and this is the main page for the course.